Experiment set4H3 for Shewanella amazonensis SB2B

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LB with Paraquat dichloride 0.03125 mg/ml

Group: stress
Media: LB + Paraquat dichloride (0.03125 mg/ml)
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Adam on 7/26/2013
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 588 D1,D2

Specific Phenotypes

For 39 genes in this experiment

For stress Paraquat dichloride in Shewanella amazonensis SB2B

For stress Paraquat dichloride across organisms

SEED Subsystems

Subsystem #Specific
Ammonia assimilation 2
DNA repair, bacterial 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Isoleucine degradation 2
Acetyl-CoA fermentation to Butyrate 1
Butanol Biosynthesis 1
DNA-replication 1
Hfl operon 1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
Multidrug Resistance Efflux Pumps 1
Peptidyl-prolyl cis-trans isomerase 1
Polyhydroxybutyrate metabolism 1
Potassium homeostasis 1
Rhamnose containing glycans 1
Transcription factors bacterial 1
Universal GTPases 1
Valine degradation 1
ZZ gjo need homes 1
n-Phenylalkanoic acid degradation 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
benzoyl-CoA biosynthesis 3 3 3
L-glutamate biosynthesis I 2 2 2
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
L-glutamine degradation II 1 1 1
L-glutamine degradation I 1 1 1
fatty acid β-oxidation I (generic) 7 6 6
oleate β-oxidation 35 33 27
ammonia assimilation cycle III 3 3 2
pyruvate fermentation to butanol II (engineered) 6 4 4
pyruvate fermentation to hexanol (engineered) 11 7 7
fatty acid β-oxidation II (plant peroxisome) 5 3 3
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
glutaryl-CoA degradation 5 3 3
2-methyl-branched fatty acid β-oxidation 14 9 8
valproate β-oxidation 9 6 5
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
fatty acid salvage 6 5 3
L-isoleucine degradation I 6 4 3
propanoate fermentation to 2-methylbutanoate 6 3 3
acetoacetate degradation (to acetyl CoA) 2 1 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 5
pyruvate fermentation to butanoate 7 3 3
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 2
adipate degradation 5 4 2
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
adipate biosynthesis 5 3 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 4
4-hydroxybenzoate biosynthesis III (plants) 5 2 2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) 5 2 2
pyruvate fermentation to butanol I 8 3 3
ketolysis 3 3 1
5-methylbenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
5-hydroxybenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
5-methoxybenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
benzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
adeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
5-methoxy-6-methylbenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
2-methyladeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 3 1
adenosylcobalamin biosynthesis from adenosylcobinamide-GDP I 3 3 1
polyhydroxybutanoate biosynthesis 3 2 1
phenyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 2 1
4-methylphenyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP 3 2 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 3
methyl ketone biosynthesis (engineered) 6 3 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 3
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
L-glutamate degradation V (via hydroxyglutarate) 10 5 3
3-phenylpropanoate degradation 10 4 3
L-glutamate and L-glutamine biosynthesis 7 6 2
benzoyl-CoA degradation I (aerobic) 7 2 2
L-valine degradation I 8 6 2
(2S)-ethylmalonyl-CoA biosynthesis 4 2 1
adenosylcobalamin biosynthesis from adenosylcobinamide-GDP II 4 2 1
L-glutamate degradation VII (to butanoate) 12 3 3
2-methylpropene degradation 8 2 2
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 3
phenylacetate degradation I (aerobic) 9 2 2
superpathway of glyoxylate cycle and fatty acid degradation 14 11 3
ketogenesis 5 3 1
L-tryptophan degradation III (eukaryotic) 15 4 3
androstenedione degradation I (aerobic) 25 6 5
methyl tert-butyl ether degradation 10 2 2
isopropanol biosynthesis (engineered) 5 1 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
pyruvate fermentation to acetone 5 1 1
ethylbenzene degradation (anaerobic) 5 1 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
glycerol degradation to butanol 16 9 3
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 3
superpathway of phenylethylamine degradation 11 3 2
superpathway of testosterone and androsterone degradation 28 6 5
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 7 3
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 3
3-hydroxypropanoate/4-hydroxybutanate cycle 18 6 3
6-gingerol analog biosynthesis (engineered) 6 2 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 7
toluene degradation VI (anaerobic) 18 3 3
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 2
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 2
4-ethylphenol degradation (anaerobic) 6 1 1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
jasmonic acid biosynthesis 19 4 3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 2
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 8 7
1-butanol autotrophic biosynthesis (engineered) 27 20 4
androstenedione degradation II (anaerobic) 27 4 4
acetyl-CoA fermentation to butanoate 7 4 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 2
mevalonate pathway I (eukaryotes and bacteria) 7 1 1
mevalonate pathway II (haloarchaea) 7 1 1
Spodoptera littoralis pheromone biosynthesis 22 4 3
superpathway of adenosylcobalamin salvage from cobinamide I 8 8 1
L-citrulline biosynthesis 8 7 1
2-deoxy-D-ribose degradation II 8 3 1
mevalonate pathway III (Thermoplasma) 8 1 1
isoprene biosynthesis II (engineered) 8 1 1
mevalonate pathway IV (archaea) 8 1 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 2
platensimycin biosynthesis 26 6 3
superpathway of adenosylcobalamin salvage from cobinamide II 9 8 1
4-oxopentanoate degradation 9 2 1
NiFe(CO)(CN)2 cofactor biosynthesis 10 5 1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 4 1
L-lysine fermentation to acetate and butanoate 10 3 1
gallate degradation III (anaerobic) 11 3 1
ethylmalonyl-CoA pathway 11 2 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 2 2
superpathway of L-citrulline metabolism 12 9 1
superpathway of cholesterol degradation III (oxidase) 49 4 4
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 21 2
sitosterol degradation to androstenedione 18 1 1
superpathway of ergosterol biosynthesis I 26 3 1
adenosylcobalamin biosynthesis II (aerobic) 33 18 1
adenosylcobalamin biosynthesis I (anaerobic) 36 18 1
superpathway of cholesterol biosynthesis 38 3 1
superpathway of L-lysine degradation 43 8 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1